This is going to be tricky to fix. When someone has a patch that updates DEPS or gyp, we need to reflect those changes before building using the chromium-ews. The problem is that this breaks the model we're using (which is updating before applying the patch). We might need some lower level hook than update-webkit-chromium so we don't actually pull new revisions from svn.webkit.org. This bug is what caused the chromium-ews to miss estade's build break (because it didn't try to build the new files he added to the gypi).
IIRC the trybots just sync again after applying the patch.
The EWS bots are git-based. Is there a way to git svn rebase with the change in the working copy?
The patch should be applied against HEAD, and applying the patch doesn't change that. You just need to update the dependencies to reflect the new DEPS and re-run gyp; all of that is svn and python scripts, even when your main checkout is git.
This was fixed a long time ago.